Biology subjects

Rachel S Schwartz

Publications and source records attributed to Rachel S Schwartz.

3 recordsLinked to original sources

bioRxiv2015

Strong Selection is Necessary for Evolution of Blindness in Cave Dwellers

Blindness has evolved repeatedly in cave-dwelling organisms, and investigating the loss of sight in cave dwellers presents an opportunity to understand the operation of fundamental evolutionary processes, including drift, selection, mutation, and migration. The observation of blind organisms has prompted many hypotheses for their blindness, including both accumulation of neutral, loss-of-function mutations and adaptation to darkness. Here we model the evolution of blindness in caves. This model captures the interaction of three forces: (1) selection favoring alleles causing blindness, (2) immigration of sightedness alleles from a surface population, and (3) loss-of-function mutations creating blindness alleles. We investigated the dynamics of this model and determined selection-strength thresholds that result in blindness evolving in caves despite immigration of sightedness alleles from the surface. Our results indicate that strong selection is required for the evolution of blindness in cave-dwelling organisms, which is consistent with recent work suggesting a high metabolic cost of eye development.

Evolutionary Biology↗

bioRxiv2015

Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions

MotivationAccurate identification of genotypes is critical in identifying de novo mutations, linking mutations with disease, and determining mutation rates. Because de novo mutations are rare, even low levels of genotyping error can cause a large fraction of false positive de novo mutations. Biological and technical processes that adversely affect genotyping include copy-number-variation, paralogous sequences, library preparation, sequencing error, and reference-mapping biases, among others.\n\nResultsWe modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models. In most cases the best model was comprised of two distributions. The major-component distribution is similar to a binomial distribution with low error and low reference bias. The minor-component distribution is overdispersed with higher error and reference bias. We also found that sites fitting the minor component are enriched for copy number variants and low complexity region. We expect that this approach to modeling the distribution of NGS data, will lead to improved genotyping. For example, this approach provides an expected distribution of reads that can be incorporated into a model to estimate de novo mutations using reads across a pedigree.\n\nAvailabilityMethods and data files are available at https://github.com/CartwrightLab/WuEtAl2016/.\n\nContactcartwright@asu.edu

Genomics↗

bioRxiv2015

Phylogenomic Reconstruction Supports Supercontinent Origins for Leishmania

Leishmania, a genus of parasites transmitted to human hosts and mammalian/reptilian reservoirs by an insect vector, is the causative agent of the human disease complex leishmaniasis. The evolutionary relationships within the genus Leishmania and its origins are the source of ongoing debate, reflected in conflicting phylogenetic and biogeographic reconstructions. This study employs a recently described bioinformatics method, SISRS, to identify over 200,000 informative sites across the genome from newly sequenced and publicly available Leishmania data. This dataset is used to reconstruct the evolutionary relationships of this genus. Additionally, we constructed a large multi-gene dataset; we used this dataset to reconstruct the phylogeny and estimate divergence dates for species. We conclude that the genus Leishmania evolved at least 90-100 million years ago. Our results support the hypothesis that Leishmania clades separated prior to, and during, the breakup of Gondwana. Additionally, we confirm that reptile-infecting Leishmania are derived from mammalian forms, and that the species that infect porcupines and sloths form a clade long separated from other species. We also firmly place the guinea-pig infecting species, L. enrietti, the globally dispersed L. siamensis, and the newly identified Australia species from kangaroos as sibling species whose distribution arises from the ancient connection between Australia, Antarctica, and South America.

Evolutionary Biology↗